As a widely applied theory that has found success across many fields, density functional theory (DFT) is largely taught. Typically, the most effective way to convey DFT concepts is through illustrative examples that are currently lacking in available resources. In this work, we demonstrate total energy calculations for H[subscript 2] using…

The process of diffusion is intimately related to random molecular displacement and is central to many problems in chemistry. Here, we provide an intuitive derivation of the diffusion equation based on the analysis of the random trajectories of particles generated and plotted by simple MATLAB and Python scripts. The codes are very simple and…

The introduction of Computational Chemistry via "Molecular Modelling and Drug Design" course at undergraduate level has opened wide possibilities for students to expand their knowledge of quantum chemistry, organic reaction mechanisms, protein-ligand interactions, drug design, and probable "in vivo" behavior of drug candidates.…

The crystalline sponge method allows for direct and precise molecular structure determination of liquid and gaseous targets and thus has been recognized as a revolutionary breakthrough in crystallography. To expose undergraduates to this cutting-edge technique, we have developed a comprehensive laboratory experiment with reaction conditions and…

The application of chemistry concepts in biological settings plays an important role in the interdisciplinary field of drug discovery and development. This is true for molecular docking, where an understanding of intermolecular forces and noncovalent interactions is useful for rational drug design and development. Here we report the design and use…

Understanding the relationship between protein structure and function can be challenging for students. Molecular visualization software aids students in this problem by allowing manipulation of structures from new and deeper perspectives. In this communication, an activity using iMolview Lite, structure visualization software for portable devices,…

Recently there is an increasing need for experiments that can be conducted remotely. In this sense, this paper presents three experiments about materials science and an X-ray diffraction (XRD) technique that can be taught and performed entirely remotely. The first experiment is about the calculation of lattice parameters, atomic radii, and…

The use of symmetry is widespread in chemistry, as it is used for predictions of the number of allowed and forbidden absorptions in electronic, vibrational, and rotational spectroscopies; for predictions of the combination of atomic orbitals to produce molecular orbitals; and in many other chemical applications. One critical step in these…

Biology and biochemistry students must learn to visualize and comprehend the complex three-dimensional (3D) structures of macromolecules such as proteins or DNA. However, most tools available for teaching biomolecular structures typically operate in two dimensions. Here, we present protocols and pedagogical approaches for using immersive augmented…

Drug design and development requires collaboration among scientists with diverse expertise. In early-stage drug design, establishment of promising drug candidates requires integration of structure-based molecular design with biopharmaceutics and ADMET (absorption, distribution, metabolism, excretion, and toxicity) principles. Much of this work is…

Visualization of three-dimensional (3D) elements has always played a huge role in chemistry education. At the same time, it is a challenge to teach with most representations being shown in two-dimensional (2D) media. With the recent rise of extended reality (XR) that includes virtual and augmented reality (VR/AR) technology in higher education,…

Molecular processes are highly complex, and are frequently difficult for high school and college students to comprehend. Because of the importance of visualization in learning, along with formative assessment of student understanding, utilization of 3D modeling software aids both educators and students alike. The activity described below required…

Visualization of chemical concepts can be challenging for many students. This is arguably a critical skill for beginning students of biochemistry to develop, since new information is often presented visually in the form of textbook figures. It is recommended that visual literacy be explicitly taught in the classroom rather than assuming that…

This laboratory class combines molecular visualization and laboratory experimentation to teach the structure of the immunoglobulins (Ig). In the first part of the class, the three-dimensional structures of the human IgG and IgM molecules available through the RCSB PDB database are visualized using freely available software. In the second part, IgG…

Herein, a slightly enhanced version of extended Huckel molecular orbital theory is applied to demonstrate the spontaneous distortion of 1,3,5,7-cyclooctatetraene from a perfect octagon, a consequence of the Jahn-Teller effect. The exercise is accessible to students who have been introduced to basic quantum mechanics and extended Huckel molecular…